Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,434,8820TG54.5% 35.4 / 53.8 33Y252S (TAC→TCC) truAtRNA pseudouridine(38‑40) synthase
Reads supporting (aligned to +/- strand):  ref base T (1/14);  new base G (18/0);  total (19/14)
Fisher's exact test for biased strand distribution p-value = 1.83e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.43e-06

GTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATAT  >  NC_000913/2434736‑2435032
                                                                                                                                                  |                                                                                                                                                      
gTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATc                                                                                                                                                    <  1:522035/151‑1 (MQ=255)
  ccATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATAACGGGCAGGGGAATcc                                                                                                                                                   >  2:140301/1‑150 (MQ=255)
  ccATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGGCCGGGGAATcc                                                                                                                                                   >  2:378147/1‑150 (MQ=255)
    atatTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCAcc                                                                                                                                                <  1:378154/151‑1 (MQ=255)
    atatTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGGAATCCAcc                                                                                                                                                >  1:295884/1‑151 (MQ=255)
      atTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGTAAGATACTAACCGTCAGGGGAAaccacc                                                                                                                                                >  1:560210/1‑149 (MQ=255)
      atTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACcg                                                                                                                                               <  1:268296/150‑1 (MQ=255)
           ccTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATAACGGGCAGGGGAATCCACcgcg                                                                                                                                             >  1:67217/1‑147 (MQ=255)
             tATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCCGTCAGGGGAATCCACCGCGAcc                                                                                                                                          >  1:230309/1‑148 (MQ=255)
              aTGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGAt                                                                                                                                      <  1:140304/151‑1 (MQ=255)
                gCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCGGGCAGGGGAATCCACCGCGACCAGaaa                                                                                                                                     >  1:307323/1‑148 (MQ=255)
                     gTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGcc                                                                                                                                <  1:223403/150‑1 (MQ=255)
                            tCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGGAGATCATACCCGGTAGGGGAAACCACCGCGCCCAGATACAGCCCCTCCGc                                                                                                                         >  2:541305/1‑150 (MQ=255)
                               tCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCCGTCAGGGGAATCCACCGCGACCAGATACAGCCCTTCCGCtttt                                                                                                                     >  2:435538/1‑151 (MQ=255)
                                  ttCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCttt                                                                                                                      <  1:64843/147‑1 (MQ=255)
                                          gTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCGGGCAGGGGAATCCACCCCGACCCGATACAACCCCTcccgatcgggagaggg                                                                                                             >  2:33932/1‑134 (MQ=255)
                                          gTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTcc                                                                                                                           <  1:33932/134‑1 (MQ=255)
                                          gTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGGAATACACCGCGACCAGATACAACCCTTCCCCTTTTTCCggt                                                                                                               >  2:633041/1‑144 (MQ=255)
                                               tACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCGGGCCGGGGAATCCACCCCGCCCCGATAAAACCCCTCCCCTTTTTCCGGTGCTtcccccc                                                                                                     >  2:512629/1‑150 (MQ=255)
                                                  gTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCCGTCAGGGGAATCCACCGCGACCAGATAAAGCCCTTCCGCTTTTTCCGTTGCTGCCCCCCGc                                                                                                   >  2:206964/1‑150 (MQ=255)
                                                       cTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGAACATAAAGGGCAGGGGAATCCACCCCGAACCGATACAACCCTTCCGCTTTTTCCGGTTCTGCCGCCCGCGGTCt                                                                                              >  2:93195/1‑150 (MQ=255)
                                                                gAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTg                                                                                      <  2:179115/149‑1 (MQ=255)
                                                                  aaTGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATAACCGGCAGGGGAATCCACCGCGACCAGATAAAACCCTTTCGCTTTTTCCGTTGCTGCCCCCCACGTTCTGTCCCTTtcc                                                                                    >  2:399753/1‑149 (MQ=255)
                                                                        ccGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCaa                                                                            <  1:257165/151‑1 (MQ=255)
                                                                         cGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAAAACATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCCTCCGCCTTTGCCGTTGCTGCCGCCAGCGGTCTGTCCTTTgccgcc                                                                                 >  1:23705/1‑145 (MQ=255)
                                                                          gAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGGCAGGGGAAACCACCGCGACCAGATACAGACCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGGTCTGTCCTTTTCCGCCAGCaa                                                                            >  1:510447/1‑149 (MQ=255)
                                                                                                ccAGAAATAGCGGGCCCATTGGCGGTTTTGGGAGGTCATACCCGTCCGGGGAATCCCCCCCGGCCCGCTAACGCCCTTCCGCCTTTGCCCTTGCTGCCCCCCGCGGTCTGTCCCTTGCCCCCCGCAACTCTTCTATCCCGCTCTcccg                                                       >  2:421202/1‑146 (MQ=255)
                                                                                                   gAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGtt                                                 <  1:25375/151‑1 (MQ=255)
                                                                                                    aaaTAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGGAATCCACCGCGACCAGATACAGACCCTCCGCTTTTGCCGTTGCTGCCGCCAGCGGTTTTTCCTTTGCCGCCAGCAAATCTGCTATCCCGCTCTCCCGCTgggt                                                 >  2:81588/1‑148 (MQ=255)
                                                                                                        aGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTgg                                             <  2:439014/150‑1 (MQ=255)
                                                                                                                    ggCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCa                                <  2:295877/151‑1 (MQ=255)
                                                                                                                             ggAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTg                        <  1:269911/150‑1 (MQ=255)
                                                                                                                                 gATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGAc                   <  1:248827/151‑1 (MQ=255)
                                                                                                                                                  tAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCatat  >  1:366805/1‑151 (MQ=255)
                                                                                                                                                  |                                                                                                                                                      
GTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATAT  >  NC_000913/2434736‑2435032

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑